From the show

Happens with Pinkie Pie and Rainbow Dash so many times it's easy to lose count, jokes about the latter's rainbow-coloured mane aside.

"Griffon the Brush Off" plays exactly like Pinkie Pie trying to vie for Rainbow Dash's attention after what seems to be her old flame shows, including Gilda violently preventing Pinkie from intruding on her time with Rainbow, and at the end, after Gilda reveals herself to be a total bitch, Rainbow reaffirming that she'd much rather be with Pinkie. It even starts with something very closely resembling Pepe le Pew chasing Penelope Pussycat, complete with Pinkie doing his little love hop.

Pinkie's Rainbow Dash obsession is revisited in later episodes; it's almost a running gag that she's Rainbow Dash's Stalker with a Crush, with Pinkie affectionately calling her "Dashie", following her damn near everywhere (particularly in "Over a Barrel" and "Party of One"), and having a severe case of No Sense of Personal Space even by Pinkie standards.

In "Party of One" the pony sent to fetch Pinkie for her surprise party is Rainbow Dash. There's a brief scene showing Rainbow Dash's face framed in the heart on Pinkie's door, which was quite possibly the closest thing the show did to a real Ship Tease in Season 1.

Rainbow Dash tries to force Pinkie Pie to move by shoving her forehead in Pinkie Pie's butt. Pinkie then sits on Dash's face and Rainbow Dash says they'll have to do it "the hard way".

"The Super Speedy Cider Squeezy 6000" opens with Rainbow Dash barging into Fluttershy's room and pulling the blanket off of her as she lies in bed, causing the latter to blush and cover her chest (albeit rather pointlessly).

"Sonic Rainboom" opens with Fluttershy recapping "the elements of a good cheer" that Rainbow Dash has been teaching her: "loss of control", "screaming and hollering", and "passion". Taken out of context, it kinda sounds like she and Rainbow Dash are talking about... something else. Not to mention that it's given out of context, with no explanation until afterwards.

"Hurricane Fluttershy" is utterly full of Ship Tease for them. Rainbow Dash can stay amazingly patient and understanding of Fluttershy's nerves, while Fluttershy can work herself up enough to overcome her fears for Rainbow's sake. One particular line from Twilight Sparkle helps seal the deal. "Do it for Rainbow Dash," indeed.

Rainbow herself at one point tells a distraught Fluttershy "But I need you!" while dramatic, emotional music plays. Then, after Fluttershy runs off, Rainbow Dash reaches out with her hoof, her disappointment and frustration mimicking a lover being disappointed in their over half.

"Dragon Quest" opens (what is it with these two and episode openings?) with Rainbow Dash and Twilight Sparkle trying to get Fluttershy to go see the dragon migration, when Rainbow Dash mentions when she and Fluttershy went to go see the butterfly migration together. Casual outing between friends, or really boring date? On top of that, Dashie has a picture of them on the migration trip together that she has been carrying around. Photo to remember the date, perhaps?

In "Dragon Quest" all the girls are viewing the dragons together, and like the others Rainbow Dash is gazing up in awe at the them, when she suddenly glances at Applejack with a sly grin on her face and scoffs. "Pretty lame move! Is that all they got?" And then the dragon tries to set her on fire.

Fluttershy and Rarity are shown to be very close even amongst the Mane Six in "Green Isn't Your Color", and Rarity seems more upset and jealous about Fluttershy's career forcing her to miss a (for lack of a better word) date with Rarity than even Fluttershy accidentally becoming part of the fashion spotlight instead of her.

Fluttershy reaches near Even the Girls Want Her status in that episode. Rarity wants her to model for her in the first place because "nopony is going to have [Fluttershy's] elegance and poise". Twilight says that "on her own Fluttershy could never do something unattractive" (hence her plan to use magic and make her do something unattractive). Photo Finish spends almost her entire appearance fan-girling over Fluttershy ("Yes! Even her sneezes are graceful!"). And the main reason Fluttershy hates being a model is the hordes of mostly female fans that flock to her wherever she goes.

As pictured above, in "Lesson Zero", Twilight Sparkle asks Rainbow Dash not to "hide her feelings" by cupping her face with both forehooves in a manner that could be interpreted romantically when taken in combination with her words.

Rainbow Dash:(to the pets) Alright, now these games will determine which one of you has the most important qualities I'm looking for in a pet. Speed, agility, guts, style. Coolness. Awesomeness. And radicalness.Twilight Sparkle: Aren't those all the same thing?Rainbow Dash: You would think that, Twilight. And that's why you would never qualify to be my pet.

In "Hearth's Warming Eve", Princess Platinum seems very close to her assistant(?) Clover the Clever. Just look at Clover's introduction:

Later, she tells Clover she doesn't mind it when Clover "stoops down" for her. Yes, she's talking about crossing a stream, but hiding implications behind stuff like this is prime Radar material, and the fact is that she then proceeds to ride Clover across said stream. On top of that, Clover is wearing a bridle, which just adds to the domination play.

After the leaders thaw out, the Pegasi and Earth ponies share hugs and high-fives. Platinum and Clover, however, nuzzle.

In "Hearts and Hooves Day", Twist gives her holiday card to a gray colt, and they hug. This visibly disappoints another filly (Tootsie Flute), who had been looking in their direction. Was that filly hoping to give her card to the colt, or to Twist? Meanwhile, yet another filly (Alula) gives her holiday card to Diamond Tiara, who seems surprised by this attention.

Bon Bon and Lyra Heartstrings, two background mares who appear together in many episodes, are widely assumed to be either best friends or a couple. Second season episodes include apparently deliberate nods to this phenomenon:

Wide shots of the town common later in "Hearts and Hooves Day" feature a number of pony pairs standing around, nearly all Stallion-Mare. However, the animators also threw in shots of Lyra and Bon Bon.

During two scenes in "A Friend In Deed", when Pinkie and a bunch of background mares are hopping across the roofs of Ponyville, Lyra & Bon Bon are shown moving in perfect unison. They are the only ponies in those scenes who do so.

In this clip of "Hurricane Fluttershy", two mares can be seen cuddling each other with big grins on their faces.

The Theme Tune Extended (included as a sing-along on the DVD The Friendship Express) has such wonderful character puns, sung from Twilight's perspective, such as "You are the Applejack of my eye".

In "A Canterlot Wedding Part 2", Twilight asks Shining Armor how he managed to get Cadence to marry him. He says that he mentioned that if she did, she'd get an "awesome sister". So Cadence married a guy just to get closer to his sister?

During the attack of the changelings, Rainbow Dash almost kisses Fluttershy on the forehead when helping her up. What sells this is that Fluttershy briefly closes her eyes as though she expected to be kissed.

In the previous episode, Twilight's first reaction to reuniting with Cadence is to wiggle her rump in her face. Sure, It Makes Sense in Context, but wow.

Twilight Sparkle is intensely reverent of Princess Celestia, well beyond even the usual level of grovelling obedience most ponies display towards her, and is utterly terrified of disappointing her or seeming "unworthy" in any way (as shown in "Swarm of the Century", "Bird in the Hoof", and especially"Lesson Zero"). Her flashback in "The Cutie Mark Chronicles" even reveals that Celestia raising the sun was " the most amazing, most wonderful thing [she's] ever seen", and was the inspiration for Twilight to pursue both magic and research as passions.

Outside show media.

In Adventures in Ponyville, when the player's (female) pony talks to any of the Mane Six, they'll sometimes say "Pony up!" to her. Unlike everything else they say to her, the speech balloon used for "Pony up!" is lined with a couple of hearts, making it seem like the Mane Six are casually flirting with the player's pony.

The German magazine comicDer Stern der Winterträume, Scanlated as The Star of Winterdreams, endswith the Mane Six sleeping together by the fireplace. Rainbow Dash is on her side, turned towards Applejack.

Look very closely at this box-art of some of the new and upcoming toys. Yes, that is Dashie looking at Pinkie Pie while their faces are framed together in a heart symbol. How subtle.